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[REVIEW]: An Introduction to Applied Bioinformatics: a free, open, and interactive text. #27

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whedon opened this Issue Aug 29, 2018 · 11 comments

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whedon commented Aug 29, 2018

Submitting author: @gregcaporaso (James Gregory Caporaso)
Repository: https://github.com/caporaso-lab/An-Introduction-To-Applied-Bioinformatics
Version: 0.1.3-dev
Editor: @tracykteal
Reviewer: @AstrobioMike
Archive: Pending

Status

status

Status badge code:

HTML: <a href="http://jose.theoj.org/papers/c16d09fe816a482881a85e4eed6f7269"><img src="http://jose.theoj.org/papers/c16d09fe816a482881a85e4eed6f7269/status.svg"></a>
Markdown: [![status](http://jose.theoj.org/papers/c16d09fe816a482881a85e4eed6f7269/status.svg)](http://jose.theoj.org/papers/c16d09fe816a482881a85e4eed6f7269)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@AstrobioMike, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/jose-reviews/invitations

The reviewer guidelines are available here: https://jose.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @tracykteal know.

Review checklist for @AstrobioMike

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source for this learning module available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
  • Version: Does the release version given match the repository release (0.1.3-dev)?
  • Authorship: Has the submitting author (@gregcaporaso) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

  • A statement of need: Do the authors clearly state the need for this module and who the target audience is?
  • Installation instructions: Is there a clearly stated list of dependencies?
  • Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

  • Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
  • Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
  • Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
  • Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
  • Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Does the paper clearly state the need for this module and who the target audience is?
  • Description: Does the paper describe the learning materials and sequence?
  • Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
  • Could someone else teach with this module, given the right expertise?
  • Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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whedon Aug 29, 2018

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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @AstrobioMike it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/jose-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/jose-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

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whedon commented Aug 29, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @AstrobioMike it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/jose-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/jose-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands
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whedon Aug 29, 2018

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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Aug 29, 2018

Attempting PDF compilation. Reticulating splines etc...
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PDF failed to compile for issue #27 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in block in find': No such file or directory (Errno::ENOENT) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:57:infind_paper_paths'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:32:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:99:in<top (required)>'
from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

'

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whedon commented Aug 29, 2018

PDF failed to compile for issue #27 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in block in find': No such file or directory (Errno::ENOENT) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:57:infind_paper_paths'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:32:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:99:in<top (required)>'
from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

'

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tracykteal Aug 29, 2018

It seems like something in the paper.md isn't allowing it to compile, but it's not clear what it is. I'll see if there's more information in error logs.

tracykteal commented Aug 29, 2018

It seems like something in the paper.md isn't allowing it to compile, but it's not clear what it is. I'll see if there's more information in error logs.

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arfon Aug 30, 2018

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It seems like something in the paper.md isn't allowing it to compile, but it's not clear what it is. I'll see if there's more information in error logs.

I think the issue is with the URL for the repository. This should be the root of the Git repository, i.e.:

https://github.com/caporaso-lab/An-Introduction-To-Applied-Bioinformatics

not 

https://github.com/caporaso-lab/An-Introduction-To-Applied-Bioinformatics/blob/master/paper.md
Member

arfon commented Aug 30, 2018

It seems like something in the paper.md isn't allowing it to compile, but it's not clear what it is. I'll see if there's more information in error logs.

I think the issue is with the URL for the repository. This should be the root of the Git repository, i.e.:

https://github.com/caporaso-lab/An-Introduction-To-Applied-Bioinformatics

not 

https://github.com/caporaso-lab/An-Introduction-To-Applied-Bioinformatics/blob/master/paper.md
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@whedon generate pdf

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arfon commented Aug 30, 2018

@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Aug 30, 2018

Attempting PDF compilation. Reticulating splines etc...
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Overall comments
I've gone through some sections in great detail (listed below), and I've looked through the rest briefly so far. Everything I've seen is very nicely done and already really well polished. And the content is stellar. For those sections I have gone through in detail, I have no problems with anything and could only think of very few suggestions that might improve things or help with clarity (to which the pull requests are linked below). Though I consider nothing I've suggested as necessary for me to happily offer my support for publication. This is clearly a well put together resource that will help many aspiring and current bioinformaticians (I'm certainly enjoying learning from it). I'm happy to continue going through sections in detail and providing my minor edits/suggestions to the repository if they are helpful, but in my opinion publication shouldn't wait until I have "fine-toothed" everything – I've certainly seen nothing I would consider problematic in the sections I've glanced through but just haven't gone through in a detailed fashion yet, and to wait for me to do so kind of feels like just waiting for a proofreader. But again that's just my opinion. Here are the sections I've covered in detail so far and links to the pull requests.

Sections covered in detail and pull requests to very minor edits/suggestions
Fundamentals: Pairwise-sequence alignments
Fundamentals: Sequence homology searching

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AstrobioMike commented Aug 30, 2018

Overall comments
I've gone through some sections in great detail (listed below), and I've looked through the rest briefly so far. Everything I've seen is very nicely done and already really well polished. And the content is stellar. For those sections I have gone through in detail, I have no problems with anything and could only think of very few suggestions that might improve things or help with clarity (to which the pull requests are linked below). Though I consider nothing I've suggested as necessary for me to happily offer my support for publication. This is clearly a well put together resource that will help many aspiring and current bioinformaticians (I'm certainly enjoying learning from it). I'm happy to continue going through sections in detail and providing my minor edits/suggestions to the repository if they are helpful, but in my opinion publication shouldn't wait until I have "fine-toothed" everything – I've certainly seen nothing I would consider problematic in the sections I've glanced through but just haven't gone through in a detailed fashion yet, and to wait for me to do so kind of feels like just waiting for a proofreader. But again that's just my opinion. Here are the sections I've covered in detail so far and links to the pull requests.

Sections covered in detail and pull requests to very minor edits/suggestions
Fundamentals: Pairwise-sequence alignments
Fundamentals: Sequence homology searching

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tracykteal Aug 31, 2018

Thanks @AstrobioMike! Given that the checklist items apply to the lessons as a whole, and you're seeing general consistency throughout, I don't think we need another reviewer for other sections. I'll just give those sections a read through as a final check.

tracykteal commented Aug 31, 2018

Thanks @AstrobioMike! Given that the checklist items apply to the lessons as a whole, and you're seeing general consistency throughout, I don't think we need another reviewer for other sections. I'll just give those sections a read through as a final check.

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gregcaporaso Sep 17, 2018

Hi @tracykteal, any updates on this? Thank you!

gregcaporaso commented Sep 17, 2018

Hi @tracykteal, any updates on this? Thank you!

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